MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments

rmRNAseq: Differential Expression Analysis for Repeated-measures RNA-seq Data

(2020) Yet Nguyen et al.   BIOINFORMATICS

A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection

(2018) Akul Singhania et al.   Nature Communications

PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects

(2018) Yuanyuan Bian et al.   BIOINFORMATICS

Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance

(2018) Brad R. Rosenberg et al.   PLoS Pathogens

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

Stan: A Probabilistic Programming Language

(2017) Bob Carpenter et al.   Journal of Statistical Software

Differential expression analysis for RNAseq using Poisson mixed models

(2017) Shiquan Sun et al.   NUCLEIC ACIDS RESEARCH

multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions

(2016) Guangliang Kang et al.   BMC BIOINFORMATICS

A 380-gene meta-signature of active tuberculosis compared with healthy controls

(2016) Simon Blankley et al.   EUROPEAN RESPIRATORY JOURNAL

A blood RNA signature for tuberculosis disease risk: a prospective cohort study

(2016) Daniel E Zak et al.   LANCET

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

PLNseq: a multivariate Poisson lognormal distribution for high-throughput matched RNA-sequencing read count data

(2015) Hong Zhang et al.   STATISTICS IN MEDICINE

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs

(2014) Mark A van de Wiel et al.   BMC BIOINFORMATICS

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

RcppArmadillo: Accelerating R with high-performance C++ linear algebra

(2013) Dirk Eddelbuettel et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

A Helicopter Perspective on TB Biomarkers: Pathway and Process Based Analysis of Gene Expression Data Provides New Insight into TB Pathogenesis

(2013) Simone A. Joosten et al.   PLoS One

Detection of Tuberculosis in HIV-Infected and -Uninfected African Adults Using Whole Blood RNA Expression Signatures: A Case-Control Study

(2013) Myrsini Kaforou et al.   PLOS MEDICINE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Misspecification of the covariance structure in generalized linear mixed models

(2012) M Chavance et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models

(2011) David A. Fournier et al.   OPTIMIZATION METHODS & SOFTWARE

Human gene expression profiles of susceptibility and resistance in tuberculosis

(2010) J Maertzdorf et al.   GENES AND IMMUNITY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The BUGS project: Evolution, critique and future directions

(2009) David Lunn et al.   STATISTICS IN MEDICINE

Bayesian Analysis of Mass Spectrometry Proteomic Data Using Wavelet-Based Functional Mixed Models

(2007) Jeffrey S. Morris et al.   BIOMETRICS